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Fixed TNG memory alignment problem and reset pointers.
2014-08-21
Magnus Lundborg
Fix
e
d TNG memory alignme
n
t
p
r
o
blem and reset pointers
.
commit
|
commitdiff
|
tree
2014-08-20
E
r
ik Lindahl
Add
_
GNU_
S
OURCE=1 to find
c
lone() w
i
th PGI
commit
|
commitdiff
|
tree
2014-08-20
R
o
land
Sch
u
lz
Change erro
r
to warning for missing OMP_N
U
M_TH
R
EADS
commit
|
commitdiff
|
tree
2014-08-20
Er
i
k Lind
a
hl
F
ix matrix
p
o
i
nter de
r
e
f
e
re
n
ce bug in update
.
c
commit
|
commitdiff
|
tree
2014-08-20
Erik
Lin
d
a
h
l
Enable SIMD
register call
i
ng convention with
g
mx_s
i
mdcall
commit
|
commitdiff
|
tree
2014-08-20
Erik
L
indah
l
Add
cycle counters for 6
4
-bit ARM
commit
|
commitdiff
|
tree
2014-08-20
Erik Lindahl
Shorten
plug
i
n
configuration message
commit
|
commitdiff
|
tree
2014-08-17
E
rik
L
i
ndahl
F
ix P
o
r
tland compiler warnings
commit
|
commitdiff
|
tree
2014-08-17
Berk
Hess
Halve
d
th
e
cost of the pull co
m
mun
i
cati
o
n
commit
|
commitdiff
|
tree
2014-08-17
Roland
S
ch
u
lz
Don't bu
i
ld tests until they are run
commit
|
commitdiff
|
tree
2014-08-16
Mark Abraham
F
i
x
gmx
t
une_pme wit
h
LJ-PM
E
commit
|
commitdiff
|
tree
2014-08-16
Mark Abraham
Fix wallcycle counting with m
d
-vv, sd and
sd2
commit
|
commitdiff
|
tree
2014-08-16
Teemu Murtola
Disable analysisd
a
ta generic tests if not compilab
l
e
commit
|
commitdiff
|
tree
2014-08-14
Berk
H
e
ss
C
o
r
r
ected
S
IMD
m
a
t
h overflow
d
ocumentation
commit
|
commitdiff
|
tree
2014-08-10
Erik Lindah
l
Improve Gromacs por
t
a
b
ility
commit
|
commitdiff
|
tree
2014-08-10
E
r
ik Lin
d
ahl
Replace __
L
P64__ with c
h
eck for pointer size
commit
|
commitdiff
|
tree
2014-08-10
Berk Hess
Added checks for
T
PI + Verl
e
t scheme
commit
|
commitdiff
|
tree
2014-08-10
R
o
l
an
d
Schulz
Check MD5sum for r
e
gressiontest
commit
|
commitdiff
|
tree
2014-08-07
Erik Lindahl
Fix portability
i
ssu
e
w
ith ArrayR
e
f initial
i
z
e
r
overloading
commit
|
commitdiff
|
tree
2014-08-07
E
r
ik Lindahl
Changed names of test f
i
les to avoid Fujitsu com
p
iler bug
commit
|
commitdiff
|
tree
2014-08-05
Ber
k
Hess
F
i
x
hang with L
J
-
P
M
E and empty domains
commit
|
commitdiff
|
tree
2014-08-05
R
o
land Schulz
W
orkar
o
und f
o
r ICC 14
commit
|
commitdiff
|
tree
2014-08-01
Erik Lindahl
Add
e
d tests
f
or denormal and
u
n
der
f
low
for
s
imd exp(
)
commit
|
commitdiff
|
tree
2014-07-28
Ro
l
and Sc
h
ulz
Fix
b
u
i
ld o
f
binary package
commit
|
commitdiff
|
tree
2014-07-28
R
ola
n
d Schu
l
z
Remove Random123/features
commit
|
commitdiff
|
tree
2014-07-25
Roland S
c
hulz
W
orkaround for ICC 14 b
u
g
commit
|
commitdiff
|
tree
2014-07-24
Roland Sch
u
lz
F
ix Cygwin+
S
hared-Libs+
F
F
T
W
commit
|
commitdiff
|
tree
2014-07-21
R
o
land S
c
hulz
Fix GMX_NONBO
N
DED_NUM_THRE
A
D
S
!=GMX_PAIRSEARCH_NUM_TH
R
EADS
commit
|
commitdiff
|
tree
2014-07-16
T
eem
u
Mur
t
o
l
a
Fix HTML help
a
n
d
man
p
ages fo
r
commands with dashes
commit
|
commitdiff
|
tree
2014-07-13
Er
i
k
Lindahl
Avoid clang/
3
2 optimization
affecting IEEE
endian detectio
n
commit
|
commitdiff
|
tree
2014-07-11
T
e
em
u
Mur
t
ola
F
i
x HTM
L
links that
contain file
ex
t
e
n
si
o
n
s
commit
|
commitdiff
|
tree
2014-07-09
Mark
A
bra
h
a
m
Qu
i
eten r
e
peated cmake r
u
ns
commit
|
commitdiff
|
tree
2014-07-09
Roland Schul
z
Fix Cygwin build
commit
|
commitdiff
|
tree
2014-07-08
Erik Li
n
dahl
Make
IEEE754 check more ro
b
u
s
t
commit
|
commitdiff
|
tree
2014-07-08
Teemu
M
urtola
M
a
ke selections ignore
\
r in input
commit
|
commitdiff
|
tree
2014-07-07
M
a
rk Abraham
F
ix tarbal
l
and install,
par
t
icularly for INSTALL
commit
|
commitdiff
|
tree
2014-07-05
Magnus Lundbo
r
g
Fix
bug ca
u
sing
reading next f
r
a
me
not to s
t
op
.
commit
|
commitdiff
|
tree
2014-07-05
Magnus Lundbo
r
g
F
i
x tng_n
u
m_frame_set
s
_get
(
) w
i
th no fram
e
sets
.
commit
|
commitdiff
|
tree
2014-07-05
Teemu Murtola
Reinstantiate unsorted index group check
commit
|
commitdiff
|
tree
2014-07-05
Roland Schul
z
Add running
tests to inst
a
ll-guide
commit
|
commitdiff
|
tree
2014-07-05
Teemu
M
u
r
tola
Update some installation-
r
elated docs
commit
|
commitdiff
|
tree
2014-07-01
Mark Abraham
Fix GMock to w
o
rk
o
n
M
S
VC
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraham
Refer to "mi
x
ed
"
p
r
e
cision in user-facing
d
o
cumentation
commit
|
commitdiff
|
tree
2014-06-29
Berk Hess
T
a
ke LJ-
P
ME
into
acc
o
unt for table
s
p
ac
i
ng
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindah
l
Fix
e
d free energy
with
LJ-PME
commit
|
commitdiff
|
tree
2014-06-29
Mark Abraha
m
Convert
install gui
d
e to mark
d
own
commit
|
commitdiff
|
tree
2014-06-29
Mark Abr
a
ham
Merge "Merge release-4-6 i
n
to release-5-0" into rel
e
ase-5-0
commit
|
commitdiff
|
tree
2014-06-29
B
erk Hess
Up
d
a
ted LJ-
P
ME documentati
o
n
commit
|
commitdiff
|
tree
2014-06-29
Rossen Ap
o
st
o
lo
v
U
se
c
o
s
istent s
t
yle when referring to force field
s
.
commit
|
commitdiff
|
tree
2014-06-29
T
eem
u
Mur
t
o
l
a
Remove some hardcode
d
s
el
e
c
ti
o
n st
r
ing
b
uffers
commit
|
commitdiff
|
tree
2014-06-29
Rolan
d
S
c
hulz
F
ix detect
i
on of i386 in tmpi
commit
|
commitdiff
|
tree
2014-06-29
Erik Lindahl
En
a
ble rtp
a
ngle/dihedral entries not co
n
nected by
.
.
.
commit
|
commitdiff
|
tree
2014-06-29
Michael Shirts
Allow p
r
inting po
t
en
t
ial energies to
dh
d
l
.
xvg
f
i
le
commit
|
commitdiff
|
tree
2014-06-29
Dav
i
d
van der Spoel
Fixes #
1
532, SEGV in g
_
current
.
commit
|
commitdiff
|
tree
2014-06-29
Roland
Sc
h
u
l
z
Merge "Mer
g
e bra
n
c
h
'release-4-6' into
r
elea
s
e-5
-
0
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Rol
a
nd Schulz
F
i
x error for no 64bit file s
u
pport
commit
|
commitdiff
|
tree
2014-06-28
E
ri
k
Lin
d
a
h
l
F
i
xed CMAP
gener
a
tion
f
or alanine dipeptide spe
c
ial
.
.
.
commit
|
commitdiff
|
tree
2014-06-28
Mag
n
us
L
undborg
Update TNG build system
commit
|
commitdiff
|
tree
2014-06-28
Mark Abraham
Use
p
a
r
allel terminology
m
ore consi
s
tently
commit
|
commitdiff
|
tree
2014-06-28
ng
o
ga
Defau
l
t SD integ
r
a
tor is now sd1
by
Ni
c
u Goga
commit
|
commitdiff
|
tree
2014-06-27
E
rik Lindahl
Always set b-
s
tate posres, even
i
f
identical to a-state
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindahl
Update g_density to handle bilayers
b
ette
r
commit
|
commitdiff
|
tree
2014-06-27
Erik Lindah
l
Fix
L
J
P
ME Lor
e
ntz-Berthelot c
o
mbi
n
ation r
u
l
e
s
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apostolov
C
h
an
g
ed link
i
ng
order to make Ext
r
a
e
work
.
commit
|
commitdiff
|
tree
2014-06-27
Er
i
k Li
n
dahl
Im
p
ro
v
e
PDB I/O (keep occupanc
y
, b-fact
o
r, element)
commit
|
commitdiff
|
tree
2014-06-27
Carsten Kutzner
R
emove obso
l
e
t
e pull-
g
eo
m
et
r
y opti
o
n 'posi
t
ion' f
r
om
.
.
.
commit
|
commitdiff
|
tree
2014-06-27
Roland Sch
u
lz
Fix Phi Platform
file fo
r
M
P
I
commit
|
commitdiff
|
tree
2014-06-27
Erik Lin
d
ahl
Avoid warnings a
b
out c
o
u
pling when fr
e
e_energy
=
no
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apo
s
tolov
Add
e
d information
a
bout d
i
hedr
a
l r
e
straint
s
.
commit
|
commitdiff
|
tree
2014-06-27
Rossen Apostolov
Remove install_manifest
.
txt during make clean
.
commit
|
commitdiff
|
tree
2014-06-26
Ma
r
k Abraham
M
e
rge "Merge release-4-6
i
nt
o
r
e
le
a
s
e-5-0" into releas
e
-5-
0
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k Lindahl
Updated Amber GBSA par
a
meters
commit
|
commitdiff
|
tree
2014-06-25
Er
i
k Lind
a
hl
Make source
c
ompile
under Linux X32 A
B
I
commit
|
commitdiff
|
tree
2014-06-25
Erik Linda
h
l
M
a
ke i
t
harder
f
or compile
r
to opti
m
ize
a
way
S
IMD CMak
e
.
.
.
commit
|
commitdiff
|
tree
2014-06-24
M
ark Abraham
Manua
l
fixes
commit
|
commitdiff
|
tree
2014-06-24
Magnu
s
L
undborg
Improved
c
heck to decide if to add
c
hain/res
i
d
ue
.
commit
|
commitdiff
|
tree
2014-06-24
Da
v
id van der
Spoel
Added check i
n
grompp for shells and input
r
ec issues
.
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Fixe
d
GROMOS
assignment of P
R
O-NH termi
n
us torsions
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Make sure d
u
plicates
bondeds
a
re set fro
m
hackblocks
commit
|
commitdiff
|
tree
2014-06-24
Erik Lindahl
Clean up C
M
AP plac
e
ment in paramete
r
list
commit
|
commitdiff
|
tree
2014-06-24
Erik Lin
d
ah
l
A
d
d
ed multisi
m
ula
t
ion info
t
o
log/output
commit
|
commitdiff
|
tree
2014-06-24
Rossen
A
postolov
Ext
e
nd versi
o
n checki
n
g
/
w
a
rn
i
ngs for checkpoint continuatio
n
commit
|
commitdiff
|
tree
2014-06-23
Ross
e
n Apostolov
Added t
i
p5
p
t
o the li
s
t of waterm
o
dels in some FF
.
commit
|
commitdiff
|
tree
2014-06-23
Erik L
i
n
dah
l
Enable 4-letter
r
esname in P
D
B outp
u
t,
k
eeps more pdbinfo
.
commit
|
commitdiff
|
tree
2014-06-23
Erik Lindahl
Detect no
n
-fatal warnings when trying CFlags for source
commit
|
commitdiff
|
tree
2014-06-23
Erik L
i
nd
a
hl
Enable xv
g
r output and labels f
o
r
g
_principal
commit
|
commitdiff
|
tree
2014-06-23
Erik Lind
a
hl
Dis
a
llow
e
xtracting V/F from XTC
f
iles in g_traj
commit
|
commitdiff
|
tree
2014-06-23
Erik Li
n
d
a
hl
Warn
i
f using nsteps
=
0
w
i
th
o
ut continuation=yes
commit
|
commitdiff
|
tree
2014-06-21
Vedran Miletić
U
s
e $
{
CMA
K
E_
I
NSTALL
_
L
I
B
D
IR} as lib directory
for
t
ng_i
o
.
.
.
commit
|
commitdiff
|
tree
2014-06-20
Berk H
e
ss
Fix g_mindist with
p
bc=XY
commit
|
commitdiff
|
tree
2014-06-20
Rossen Apostolov
Fix
e
d typo in oplsaa ASPH charges
.
commit
|
commitdiff
|
tree
2014-06-20
R
o
ssen
A
p
o
s
tolov
Removed un
u
sed param
e
t
e
rs and cleanup of inputr
e
c
.
commit
|
commitdiff
|
tree
2014-06-19
Roland Schulz
F
i
x
r
ef
error
i
n constra
i
nt
p
ull c
o
d
e
commit
|
commitdiff
|
tree
2014-06-19
R
o
ssen A
p
os
t
olov
Small typos in surface tensi
o
n
d
e
s
cription
.
commit
|
commitdiff
|
tree
2014-06-19
Mag
n
us Lu
n
d
borg
Bum
p
ed the TNG library to t
h
e latest v
e
r
s
ion
.
commit
|
commitdiff
|
tree
2014-06-18
E
ri
k
Lindahl
Fixed CMake 2
.
8
.
12+ CUD
A
dylib bugs
a
nd warnings on
.
.
.
commit
|
commitdiff
|
tree
2014-06-18
Ros
s
en Apostolov
A
dd
e
d referenc
e
to cmap in pdb2g
m
x
.
commit
|
commitdiff
|
tree
2014-06-18
Berk Hess
Fixed
sig
n
error i
n
pos
r
es dvdl
commit
|
commitdiff
|
tree
2014-06-18
Mark Ab
r
aham
Made mdrun warn when
g
eneri
c
k
ernels are used
commit
|
commitdiff
|
tree
2014-06-17
Car
l
o
C
a
m
illoni
Fix
a Repl
i
ca
E
xchange o
u
tpu
t
pro
b
lem
commit
|
commitdiff
|
tree
next